Applications/bamstats

Bamstats

Calculate statistics on BAM file insert sizes. Help output below, more detailed information can be found here’. Darcs source code repository at http://malde.org/~ketil/biohaskell/bamstats/.

bam v0.3, ©2012 Ketil Malde

bam [COMMAND] ... [OPTIONS]
  Extract information from BAM files

Common flags:
  -? --help         Display help message
  -V --version      Print version information

bam stats [OPTIONS] [BAM file(s)]
  Calculate statistics on insert sizes

  -n --numrd=INT    max number of reads (default: all)

bam hist [OPTIONS] [BAM file(s)]
  Collect a histogram of insert sizes

  -n --numrd=INT    max number of reads to include
  -b --bins=INT     number of bins
  -m --maxdist=INT  max insert size to count
  -p --plot[=ITEM]  gnuplot output, with optional gnuplot commands

bam quants [OPTIONS] [BAM file(s)]
  output approximate quantiles instead of the full histogram

  -n --numrd=INT    max number of reads to include
  -m --mindist=INT  minimum insert size to count
  -d --delta=FLOAT  relative size of next bin

bam dump [OPTIONS] [BAM file(s)]
  Dump alignments in the different classes.

  -n --numrd=INT    max number of reads (default: 100)